Modeling Protein Flexibility in Molecular Docking

Abstract

Protein flexibility plays an important role in carrying out protein functions. However, computational modeling of protein flexibility in binding events is of great challenge because proteins have large internal degrees of freedom. In this chapter, the computational methods for modeling protein flexibility in protein-ligand docking and protein-protein docking are classified into three groups, soft docking, induced-fit docking and ensemble docking; each class is reviewed in detail. The chapter has also reviewed the methods for modeling protein flexibility in the post-docking stage of protein-protein docking and protein-ligand docking, and the recent progress for modeling peptide flexibility in the emerging protein-peptide docking.